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  1. Gibberellins are well known for their growth control function in flower, fruit and seed development, and as such, exogenous gibberellic acid (GA) application plays an important role in viticulture. Unfortunate...

    Authors: Chenxia Cheng, Chen Jiao, Stacy D Singer, Min Gao, Xiaozhao Xu, Yiming Zhou, Zhi Li, Zhangjun Fei, Yuejin Wang and Xiping Wang
    Citation: BMC Genomics 2015 16:128
    Content type: Research article Published on:

  2. Many species of the genus Prevotella are pathogens that cause oral diseases. Prevotella intermedia is known to cause various oral disorders e.g. periodontal disease, periapical periodontitis and noma as well as c...

    Authors: Yunfeng Ruan, Lu Shen, Yan Zou, Zhengnan Qi, Jun Yin, Jie Jiang, Liang Guo, Lin He, Zijiang Chen, Zisheng Tang and Shengying Qin
    Citation: BMC Genomics 2015 16:122
    Content type: Research article Published on:

  3. microRNAs (miRNAs) are important regulators of translation and have been implicated in the pathogenesis of a number of cardiovascular diseases, including stroke, and suggested as possible prognostic biomarkers...

    Authors: Anne Holt Müller, Gro Klitgaard Povlsen, Claus Heiner Bang-Berthelsen, Lars Schack Kruse, Janne Nielsen, Karin Warfvinge and Lars Edvinsson
    Citation: BMC Genomics 2015 16:119
    Content type: Research article Published on:

  4. Extensive focus is placed on the comparative analyses of consensus genotypes in the study of West Nile virus (WNV) emergence. Few studies account for genetic change in the underlying WNV quasispecies populatio...

    Authors: Cornell Kortenhoeven, Fourie Joubert, Armanda DS Bastos and Celia Abolnik
    Citation: BMC Genomics 2015 16:118
    Content type: Methodology article Published on:

  5. In plants, RNA silencing plays a fundamental role as defence mechanism against viruses. During last years deep-sequencing technology has allowed to analyze the sRNA profile of a large variety of virus-infected...

    Authors: Mari Carmen Herranz, Jose Antonio Navarro, Evelien Sommen and Vicente Pallas
    Citation: BMC Genomics 2015 16:117
    Content type: Research article Published on:

  6. NdgR is an IclR-type transcription factor that regulates leucine biosynthesis and other metabolic pathways in Streptomyces coelicolor. Recent study revealed that NdgR is one of the regulatory targets of SigR, an ...

    Authors: Ji-Nu Kim, Yujin Jeong, Ji Sun Yoo, Jung-Hye Roe, Byung-Kwan Cho and Byung-Gee Kim
    Citation: BMC Genomics 2015 16:116
    Content type: Research article Published on:

  7. The paradigm of resistance evolution to chemotherapeutic agents is that a key coding mutation in a specific gene drives resistance to a particular drug. In the case of resistance to the anti-malarial drug chlo...

    Authors: Geoffrey H Siwo, Asako Tan, Katrina A Button-Simons, Upeka Samarakoon, Lisa A Checkley, Richard S Pinapati and Michael T Ferdig
    Citation: BMC Genomics 2015 16:115
    Content type: Research article Published on:

  8. Social plasticity is a pervasive feature of animal behavior. Animals adjust the expression of their social behavior to the daily changes in social life and to transitions between life-history stages, and this ...

    Authors: José M Simões, Eduardo N Barata, Rayna M Harris, Lauren A O’Connell, Hans A Hofmann and Rui F Oliveira
    Citation: BMC Genomics 2015 16:114
    Content type: Research article Published on:

  9. Recent studies have shown that some pseudogenes are transcribed and contribute to cancer when dysregulated. In particular, pseudogene transcripts can function as competing endogenous RNAs (ceRNAs). The high si...

    Authors: Joshua D Welch, Jeanette Baran-Gale, Charles M Perou, Praveen Sethupathy and Jan F Prins
    Citation: BMC Genomics 2015 16:113
    Content type: Research article Published on:

  10. Many northern-hemisphere forests are dominated by oaks. These species extend over diverse environmental conditions and are thus interesting models for studies of plant adaptation and speciation. The genomic to...

    Authors: Isabelle Lesur, Grégoire Le Provost, Pascal Bento, Corinne Da Silva, Jean-Charles Leplé, Florent Murat, Saneyoshi Ueno, Jerôme Bartholomé, Céline Lalanne, François Ehrenmann, Céline Noirot, Christian Burban, Valérie Léger, Joelle Amselem, Caroline Belser, Hadi Quesneville…
    Citation: BMC Genomics 2015 16:112
    Content type: Research article Published on:

  11. Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating rice disease worldwide. Xa39 is a resistance (R) gene with a broad-spectrum hypersensitive response (BSHR) to Xoo. Nevertheless, t...

    Authors: Fan Zhang, Li-Yu Huang, Fan Zhang, Jauhar Ali, Casiana Vera Cruz, Da-Long Zhuo, Zheng-Lin Du, Zhi-kang Li and Yong-Li Zhou
    Citation: BMC Genomics 2015 16:111
    Content type: Research article Published on:

  12. Members of Comamonas testosteroni are environmental microorganisms that are usually found in polluted environment samples. They utilize steroids and aromatic compounds but rarely sugars, and show resistance to mu...

    Authors: Lin Liu, Wentao Zhu, Zhan Cao, Biao Xu, Gejiao Wang and Meizhong Luo
    Citation: BMC Genomics 2015 16:110
    Content type: Research article Published on:

  13. Epistasis (synergistic interaction) among SNPs governing gene expression is likely to arise within transcriptional networks. However, the power to detect it is limited by the large number of combinations to be...

    Authors: Darren J Fitzpatrick, Colm J Ryan, Naisha Shah, Derek Greene, Cliona Molony and Denis C Shields
    Citation: BMC Genomics 2015 16:109
    Content type: Research article Published on:

  14. One of the reasons hard red winter wheat cultivar ‘Duster’ (PI 644016) is widely grown in the southern Great Plains is that it confers a consistently high level of resistance to biotype GP of Hessian fly (Hf)....

    Authors: Genqiao Li, Ying Wang, Ming-Shun Chen, Erena Edae, Jesse Poland, Edward Akhunov, Shiaoman Chao, Guihua Bai, Brett F Carver and Liuling Yan
    Citation: BMC Genomics 2015 16:108
    Content type: Research article Published on:

  15. Meiotic recombination has traditionally been explained based on the structural requirement to stabilize homologous chromosome pairs to ensure their proper meiotic segregation. Competing hypotheses seek to expl...

    Authors: Caitlin R Ross, Dominick S DeFelice, Greg J Hunt, Kate E Ihle, Gro V Amdam and Olav Rueppell
    Citation: BMC Genomics 2015 16:107
    Content type: Research article Published on:

  16. Ophiocordyceps sinensis, a worm and fungus combined mixture which Hirsutella sinensis is parasitic on the caterpillar body, has been used as a traditional medicine or healthy food in China for ...

    Authors: Zhi-Qiang Liu, Shan Lin, Peter James Baker, Ling-Fang Wu, Xiao-Rui Wang, Hui Wu, Feng Xu, Hong-Yan Wang, Mgavi Elombe Brathwaite and Yu-Guo Zheng
    Citation: BMC Genomics 2015 16:106
    Content type: Research article Published on:

  17. Pea (Pisum sativum L.), a major pulse crop grown for its protein-rich seeds, is an important component of agroecological cropping systems in diverse regions of the world. New breeding challenges imposed by global...

    Authors: Judith Burstin, Pauline Salloignon, Marianne Chabert-Martinello, Jean-Bernard Magnin-Robert, Mathieu Siol, Françoise Jacquin, Aurélie Chauveau, Caroline Pont, Grégoire Aubert, Catherine Delaitre, Caroline Truntzer and Gérard Duc
    Citation: BMC Genomics 2015 16:105
    Content type: Research Article Published on:

  20. Epigenetic modifications play important roles in the regulation of plant development. DNA methylation is an important epigenetic modification that dynamically regulates gene expression during developmental pro...

    Authors: Jihong Hu, Xiaojun Chen, Hongyuan Zhang and Yi Ding
    Citation: BMC Genomics 2015 16:102
    Content type: Research article Published on:

  21. The anthers and pollen grains are critical for male fertility and hybrid rice breeding. The development of rice mature anther and pollen consists of multiple continuous stages. However, molecular mechanisms re...

    Authors: Sheng Ling, Caisheng Chen, Yang Wang, Xiaocong Sun, Zhanhua Lu, Yidan Ouyang and Jialing Yao
    Citation: BMC Genomics 2015 16:101
    Content type: Research article Published on:

  22. Small RNAs include different classes essential for endogenous gene regulation and cellular defence against genomic parasites. However, a comprehensive analysis of the small RNA pathways in the germline of the ...

    Authors: Leandro Castellano, Ermanno Rizzi, Jonathan Krell, Manlio Di Cristina, Roberto Galizi, Ayako Mori, Janis Tam, Gianluca De Bellis, Justin Stebbing, Andrea Crisanti and Tony Nolan
    Citation: BMC Genomics 2015 16:100
    Content type: Research article Published on:

  24. Pistachio (Pistacia vera L.) is a dioecious species that has a long juvenility period. Therefore, development of marker-assisted selection (MAS) techniques would greatly facilitate pistachio cultivar-breeding pro...

    Authors: Salih Kafkas, Mortaza Khodaeiaminjan, Murat Güney and Ebru Kafkas
    Citation: BMC Genomics 2015 16:98
    Content type: Research article Published on:

  25. RNA-Seq has become increasingly popular in transcriptome profiling. One aspect of transcriptome research is to quantify the expression levels of genomic elements, such as genes, their transcripts and exons. Ac...

    Authors: Shanrong Zhao and Baohong Zhang
    Citation: BMC Genomics 2015 16:97
    Content type: Research article Published on:

  26. Interferons (IFN) are cytokines secreted by vertebrate cells involved in activation of signaling pathways that direct the synthesis of antiviral genes. To gain a global understanding of antiviral genes induced...

    Authors: Cheng Xu, Øystein Evensen and Hetron Mweemba Munang’andu
    Citation: BMC Genomics 2015 16:96
    Content type: Research article Published on:

  27. MicroRNAs (miRNAs) represent new and potentially informative diagnostic targets for disease detection and prognosis. However, little work exists documenting the effect of TRIzol, a common viral inactivation an...

    Authors: Janice Duy, Jeffrey W Koehler, Anna N Honko and Timothy D Minogue
    Citation: BMC Genomics 2015 16:95
    Content type: Methodology article Published on:

  28. The protozoan Eimeria tenella is a common parasite of chickens, causing avian coccidiosis, a disease of on-going concern to agricultural industries. The high prevalence of E. tenella can be attributed to the resi...

    Authors: Robert A Walker, Philippa A Sharman, Catherine M Miller, Christoph Lippuner, Michal Okoniewski, Ramon M Eichenberger, Chandra Ramakrishnan, Fabien Brossier, Peter Deplazes, Adrian B Hehl and Nicholas C Smith
    Citation: BMC Genomics 2015 16:94
    Content type: Research article Published on:

  29. Brucellosis is an important zoonotic disease that affects both humans and animals. We sequenced the full genome and characterised the genetic diversity of two Brucella melitensis isolates from Malaysia and the Ph...

    Authors: Kim-Kee Tan, Yung-Chie Tan, Li-Yen Chang, Kok Wei Lee, Siti Sarah Nore, Wai-Yan Yee, Mohd Noor Mat Isa, Faizatul Lela Jafar, Chee-Choong Hoh and Sazaly AbuBakar
    Citation: BMC Genomics 2015 16:93
    Content type: Research article Published on:

  30. The 1000 Genome project paved the way for sequencing diverse human populations. New genome projects are being established to sequence underrepresented populations helping in understanding human genetic diversi...

    Authors: Gaurav Thareja, Sumi Elsa John, Prashantha Hebbar, Kazem Behbehani, Thangavel Alphonse Thanaraj and Osama Alsmadi
    Citation: BMC Genomics 2015 16:92
    Content type: Research article Published on:

  31. 20(S)-hydroxycholesterol (20(S)) potentially reduces adipogenesis in mammalian cells. The role of this oxysterol and molecular mechanisms underlying the adipogenesis of preadipocytes from laying hens have not ...

    Authors: Alemu Regassa and Woo Kyun Kim
    Citation: BMC Genomics 2015 16:91
    Content type: Research article Published on:

  32. The genome of pathogenic Leptospira interrogans contains two chromosomes. Plasmids and prophages are known to play specific roles in gene transfer in bacteria and can potentially serve as efficient genetic tools ...

    Authors: Weinan Zhu, Jin Wang, Yongzhang Zhu, Biao Tang, Yunyi Zhang, Ping He, Yan Zhang, Boyu Liu, Xiaokui Guo, Guoping Zhao and Jinhong Qin
    Citation: BMC Genomics 2015 16:90
    Content type: Research article Published on:

  33. Crossing over assures the correct segregation of the homologous chromosomes to both poles of the dividing meiocyte. This exchange of DNA creates new allelic combinations thus increasing the genetic variation p...

    Authors: Antoine Ederveen, Yuching Lai, Marc A van Driel, Tom Gerats and Janny L Peters
    Citation: BMC Genomics 2015 16:89
    Content type: Research article Published on:

  34. The pig, which shares greater similarities with human than with mouse, is important for agriculture and for studying human diseases. However, similarities in the genetic architecture and molecular regulations ...

    Authors: Jun Zhu, Congying Chen, Bin Yang, Yuanmei Guo, Huashui Ai, Jun Ren, Zhiyu Peng, Zhidong Tu, Xia Yang, Qingying Meng, Stephen Friend and Lusheng Huang
    Citation: BMC Genomics 2015 16:88
    Content type: Research article Published on:

  35. Because species-specific gene expression is driven by species-specific regulation, understanding the relationship between sequence and function of the regulatory regions in different species will help elucidat...

    Authors: Olgert Denas, Richard Sandstrom, Yong Cheng, Kathryn Beal, Javier Herrero, Ross C Hardison and James Taylor
    Citation: BMC Genomics 2015 16:87
    Content type: Research Published on:

  36. Annona squamosa L., a popular fruit tree, is the most widely cultivated species of the genus Annona. The lack of transcriptomic and genomic information limits the scope of genome investigations...

    Authors: Yogesh Gupta, Ashish K Pathak, Kashmir Singh, Shrikant S Mantri, Sudhir P Singh and Rakesh Tuli
    Citation: BMC Genomics 2015 16:86
    Content type: Research article Published on:

  37. Over the last decade, emerging research methods, such as comparative genomic analysis and phylogenetic study, have yielded new insights into genotypes and phenotypes of closely related bacterial strains. Sever...

    Authors: Jianping Jiang, Jianlei Gu, Liang Zhang, Chenyi Zhang, Xiao Deng, Tonghai Dou, Guoping Zhao and Yan Zhou
    Citation: BMC Genomics 2015 16:85
    Content type: Methodology article Published on:

  38. Alzheimer’s disease (AD) is a complex, irreversible neurodegenerative disorder. At present there are neither reliable markers to diagnose AD at an early stage nor therapy. To investigate underlying disease mec...

    Authors: Amir M Hossini, Matthias Megges, Alessandro Prigione, Bjoern Lichtner, Mohammad R Toliat, Wasco Wruck, Friederike Schröter, Peter Nuernberg, Hartmut Kroll, Eugenia Makrantonaki, Christos C Zoubouliss and James Adjaye
    Citation: BMC Genomics 2015 16:84
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2015 16:433

  39. Targeting Induced Local Lesions IN Genomes (TILLING) is a reverse genetics approach to directly identify point mutations in specific genes of interest in genomic DNA from a large chemically mutagenized populat...

    Authors: Luyuan Pan, Arish N Shah, Ian G Phelps, Dan Doherty, Eric A Johnson and Cecilia B Moens
    Citation: BMC Genomics 2015 16:83
    Content type: Methodology article Published on:

  40. Reverse transcription quantitative PCR (RT-qPCR) is considered the gold standard for quantifying relative gene expression. Normalization of RT-qPCR data is commonly achieved by subtracting the Ct values of the in...

    Authors: Xiangqin Cui, Shaohua Yu, Ashutosh Tamhane, Zenoria L Causey, Adam Steg, Maria I Danila, Richard J Reynolds, Jinyi Wang, Keith C Wanzeck, Qi Tang, Stephanie S Ledbetter, David T Redden, Martin R Johnson and S Louis Bridges Jr.
    Citation: BMC Genomics 2015 16:82
    Content type: Methodology article Published on:

  41. Nuclear receptors have crucial roles in all metazoan animals as regulators of gene transcription. A wide range of studies have elucidated molecular and biological significance of nuclear receptors but there ar...

    Authors: Christiane Eichner, Sussie Dalvin, Rasmus Skern-Mauritzen, Ketil Malde, Heidi Kongshaug and Frank Nilsen
    Citation: BMC Genomics 2015 16:81
    Content type: Research article Published on:

  42. Social amoebae are lower eukaryotes that inhabit the soil. They are characterized by the construction of a starvation-induced multicellular fruiting body with a spore ball and supportive stalk. In most species...

    Authors: Hideko Urushihara, Hidekazu Kuwayama, Kensuke Fukuhara, Takehiko Itoh, Hiroshi Kagoshima, Tadasu Shin-I, Atsushi Toyoda, Kazuyo Ohishi, Tateaki Taniguchi, Hideki Noguchi, Yoko Kuroki, Takashi Hata, Kyoko Uchi, Kurato Mohri, Jason S King, Robert H Insall…
    Citation: BMC Genomics 2015 16:80
    Content type: Research article Published on:

  43. Influenza viruses exist as a large group of closely related viral genomes, also called quasispecies. The composition of this influenza viral quasispecies can be determined by an accurate and sensitive sequenci...

    Authors: Silvie Van den Hoecke, Judith Verhelst, Marnik Vuylsteke and Xavier Saelens
    Citation: BMC Genomics 2015 16:79
    Content type: Research article Published on:

  44. The ribosome translates mRNA to protein with the aid of a number of accessory protein factors. Translational GTPases (trGTPases) are an integral part of the ‘core set’ of essential translational factors, and a...

    Authors: Gemma Catherine Atkinson
    Citation: BMC Genomics 2015 16:78
    Content type: Research article Published on:

  45. Disease resistance (R) genes from different Rosaceae species have been identified by map-based cloning for resistance breeding. However, there are few reports describing the pattern of R-gene evolution in Rosacea...

    Authors: Yan Zhong, Huan Yin, Daniel James Sargent, Mickael Malnoy and Zong-Ming (Max) Cheng
    Citation: BMC Genomics 2015 16:77
    Content type: Research article Published on:

  46. Spi-B and PU.1 are highly related members of the E26-transformation-specific (ETS) family of transcription factors that have similar, but not identical, roles in B cell development. PU.1 and Spi-B are both exp...

    Authors: Lauren A Solomon, Stephen KH Li, Jan Piskorz, Li S Xu and Rodney P DeKoter
    Citation: BMC Genomics 2015 16:76
    Content type: Research article Published on:

  47. Larvae of the tenebrionids Tenebrio molitor and Tribolium castaneum have highly compartmentalized guts, with primarily cysteine peptidases in the acidic anterior midgut that contribute to the early stages of prot...

    Authors: Alexander G Martynov, Elena N Elpidina, Lindsey Perkin and Brenda Oppert
    Citation: BMC Genomics 2015 16:75
    Content type: Research article Published on:

  48. The moon jellyfish Aurelia aurita is a widespread scyphozoan species that forms large seasonal blooms. Here we provide the first comprehensive view of the entire complex life of the Aurelia Red Sea strain by empl...

    Authors: Vera Brekhman, Assaf Malik, Brian Haas, Noa Sher and Tamar Lotan
    Citation: BMC Genomics 2015 16:74
    Content type: Research article Published on:

  49. Bacillus methanolicus MGA3 is a thermophilic, facultative ribulose monophosphate (RuMP) cycle methylotroph. Together with its ability to produce high yields of amino acids, the relevance of thi...

    Authors: Marta Irla, Armin Neshat, Trygve Brautaset, Christian Rückert, Jörn Kalinowski and Volker F Wendisch
    Citation: BMC Genomics 2015 16:73
    Content type: Research article Published on:

  50. The RNA steady-state levels in the cell are a balance between synthesis and degradation rates. Although transcription is important, RNA processing and turnover are also key factors in the regulation of gene ex...

    Authors: Vânia Pobre and Cecília M Arraiano
    Citation: BMC Genomics 2015 16:72
    Content type: Research article Published on:

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BMC Genomics

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